rs10515666

chr5-152400985-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020167.5(NMUR2):c.727-2841T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0711 in 152,288 control chromosomes in the GnomAD database, including 759 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.071 (759 hom., cov: 32)
• Consequence: NMUR2 NM_020167.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.588

Genes affected

NMUR2 (HGNC:16454): (neuromedin U receptor 2) This gene encodes a protein from the G-protein coupled receptor 1 family. This protein is a receptor for neuromedin U, which is a neuropeptide that is widely distributed in the gut and central nervous system. This receptor plays an important role in the regulation of food intake and body weight. [provided by RefSeq, Jul 2008]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.198 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NMUR2	NM_020167.5	c.727-2841T>C		intron_variant		ENST00000255262.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NMUR2	ENST00000255262.4	c.727-2841T>C		intron_variant		1	NM_020167.5	P1
	ENST00000663819.1	n.183+25772A>G		intron_variant, non_coding_transcript_variant
NMUR2	ENST00000518933.1	n.273-2841T>C		intron_variant, non_coding_transcript_variant		3
	ENST00000663460.1	n.216+25772A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0711 AC: 10816 AN: 152170 Hom.: 755 Cov.: 32

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.0346

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.0631

Gnomad FIN AF: 0.0249

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.00619

Gnomad OTH AF: 0.0540

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0711 AC: 10834 AN: 152288 Hom.: 759 Cov.: 32 AF XY: 0.0746 AC XY: 5559 AN XY: 74476

Gnomad4 AFR AF: 0.155

Gnomad4 AMR AF: 0.135

Gnomad4 ASJ AF: 0.0346

Gnomad4 EAS AF: 0.209

Gnomad4 SAS AF: 0.0628

Gnomad4 FIN AF: 0.0249

Gnomad4 NFE AF: 0.00619

Gnomad4 OTH AF: 0.0539

Alfa AF: 0.0332 Hom.: 66

Bravo AF: 0.0832

Asia WGS AF: 0.140 AC: 486 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	1.3
Dann	Benign	0.38

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10515666; hg19: chr5-151780546;